Genomics Education Alliance

Developed by Dr. Vince Buonaccorsi at Juniata College, the GCAT-SEEK Eukaryotic Genomics Workshop Manual consists of seven chapters that cover genome assembly, gene annotations, and variant calling:

1. Genome assembly I: Quality control with FastQC and Trimmomatic
2. Genome assembly II: Assembly size estimation and k-mer graphs
3. Genome assembly III: Assembly algorithms
4. Genome annotation with Maker I: Overview and repeat finding
5. Genome annotation with Maker II: Whole genome analysis
6. Whole genome annotation: Miscellaneous methods
7. SNP calling and interpretation

CourseSource Publication

Buonaccorsi, V.P., Hamlin, D., Fowler, B., Sullivan, C., and Sickler, A. 2017. An Introduction to Eukaryotic Genome Analysis in Non-model Species for Undergraduates: A tutorial from the Genome Consortium for Active Teaching. CourseSource. https://doi.org/10.24918/cs.2017.1

Developed by Dr. Mark Peterson, this module provides an overview of the different types of RNA-Seq data analyses. It describes how to assess the quality of RNA-Seq data with FastQC, trim adapters and low quality data with Trimmomatic, read mapping with RSEM, differential expression analysis with DESeq, variant detection with VarScan, and de novo assembly with Trinity.

CourseSource Publication

Peterson, M.P., Malloy, J.T., Buonaccorsi, V.P., and Marden, J.H. 2015. Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching. CourseSource. https://doi.org/10.24918/cs.2015.14